Journal: Methods in molecular biology (Clifton, N.J.)

Article Title: Mass Cytometry Assessment of Cell Phenotypes and Signaling States in Human Whole Blood

doi: 10.1007/978-1-0716-2553-8_10

Figure Lengend Snippet: Whole blood phosphoflow panel 1

Article Snippet: 142 Nd cCasp3 D3E9 Fluidigm 3142004A 143 Nd CD19 HIB19 Biolegend 302202 144 Nd pPLCg2 [Y759] K86-689.37 Fluidigm 3144015A 145 Nd CD4 RPA-T4 Fluidigm 3145001B 146 Nd IgD IA6-2 Fluidigm 3146005B 147 Sm CD20 2H7 Fluidigm 3147001B 148 Nd IgA Polyclonal Fluidigm 3148007B 149 Sm CD25 2A3 Fluidigm 3149010B 150 Nd pStat5 [Y694] 47 Fluidigm 3150005A 151 Eu CD123 6H6 Fluidigm 3151001B 153 Eu pStat1 [Y701] 4a Fluidigm 3153005A 154 Sm CD45 HI30 Fluidigm 3154001B 155Gd CD27 L128 Fluidigm 3155001B 156 Gd p38 [T180/Y182] D3F9 Fluidigm 3156002A 157 Gd CD24 ML-5 Biolegend 311102 158 Gd pStat3 [Y705] 4/P-Stat3 Fluidigm 3158005A 159Tb CD11c Bu15 Fluidigm 3159001B 160Gd CD14 M5E2 Fluidigm 3160001B 161 Dy CD141(BDCA-3) AD5-14H12 Miltenyi 130-090-694 162 Dy CD66b 80H3 Fluidigm 3162023B 163 Dy CD56 NCAM16.2 Fluidigm 3163007B 164 Dy IkBa L35A5 Fluidigm 3164004A 165 Ho pCREB [S133] 87G3 Fluidigm 3165009A 166 Er CD16 B73.1 Biolegend 360702 167 Er CD38 HIT2 Fluidigm 3167001B 168 Er CD8 SK1 Fluidigm 3168002B 169 Tm CD45RA HI100 Fluidigm 3169008B 170 Er CD3 UCHT1 Fluidigm 3170001B 171 Yb pERK1/2 [T202/Y204] D13.14.4E Fluidigm 3171010A 172 Yb Anti-Ki-67 B56 Fluidigm 3172024B 174 Yb HLA-DR L243 Fluidigm 3174001B 175Lu CD7 CD7-6B7 Biolegend 343102 176 Yb CD127/IL-7Ra P48-48 Novus Bio MAB306-100 209Bi CD11b/Mac-1 ICRF44 Fluidigm 3209003B Open in a separate window 1 Open channels are not shown but include Pd channels, Cd channel, Pt channels, 89Y,152Sm and 173Yb Whole blood phosphoflow panel1.

Techniques:

Journal: Nature Communications

Article Title: Skin basal cell carcinomas assemble a pro-tumorigenic spatially organized and self-propagating Trem2+ myeloid niche

doi: 10.1038/s41467-023-37993-w

Figure Lengend Snippet: a Merged UMAP plot of scRNA-Seq data of HLA-DRA + cells ( n = 4 independent tumors). b Feature plots for CD207, ITGAM , CD68 , and TREM2 from the UMAP that is shown in a . c UMAP plot of scRNA-Seq data of HLA-DRA + cells from an individual sample. d Feature plots for CD207 , ITGAM , CD68 , and TREM2 from the UMAP that is shown in c . e CyTOF study design for examining human BCC tumor single-cell suspensions. f TSNE plot of the merged CD45 + cells from BCC samples. g Feature plots for the key CD3 + and HLA-DR + clusters within the CD45 + fraction. h Quantification of the proportions of CD3 + , HLA-DR + , and other cell types by sample. i Feature plots for CD11b, CD206, and TREM2 from the subset of HLA-DR + cells. j Quantification of the percentages of cells that are HLA-DR + CD11b + , HLA-DR + CD11b + TREM2 + , and HLA-DR + CD11b + TREM2 + Ki67 + . For f , h , i , j , n = 13 independent tumors. Source data are provided as a Source data file.

Article Snippet: Additional surface marker antibodies were CD45-89Y (Fluidigm; 3089003B), CD207-175Lu (Fluidigm; 3175016B), CD279-155Gd (Fluidigm; 3155009B), CD8a-146Nd (Fluidigm; 3146001B), TIM-3-153Eu (Fluidigm; 3153008B), TIGIT-209Bi (Fluidigm; 3209013B), and CD274-156Gd (Fluidigm; 3156026B).

Techniques:

Journal: Nature Communications

Article Title: Skin basal cell carcinomas assemble a pro-tumorigenic spatially organized and self-propagating Trem2+ myeloid niche

doi: 10.1038/s41467-023-37993-w

Figure Lengend Snippet: a UMAP plot of scRNA-Seq data of Cd45 + sorted cells from mouse BCC tumor ( n = 1 primary tumor). b UMAP plot of scRNA-Seq data of myeloid cells from a . c UMAP plot of scRNA-Seq data of mature myeloid cells from b . d Heatmap showing the top 10 marker genes for the various clusters from c . e Stacked violin plot of various key myeloid-associated markers for each of the clusters from c . f Quantification of the flow cytometry confirmation analysis of the myeloid cells from mBCC. g Monocle analysis of the myeloid cells from c . h Diagram of M1 and M2 polarization experiments to generate M1 and M2 polarization scores. Top 20 differential genes between the M1- and M2-polarized cells were extracted and used for scoring. Feature plot of the M1- and M2-associated polarization scoring for clustering from c . i Spatial locations of Cd68 + Trem2 + cells within mouse BCCs relative to the proliferative Ly6d - tumor epithelium. RNAScope is for Cd68 (magenta), Trem2 (green), and protein staining is for K14-protein (white), Ki67-protein (red), and Ly6d -RNA (yellow). Red arrows show some Ki67 + cells. Green arrows some show Cd68 + Trem2 + cells. Dotted yellow line indicates Ly6d + region. Quantification of average cell distances of individual Cd68 + Trem2 + cells. Scale bar = 50 μm. For f , i , n = 3 independent tumors. Error bars represent mean +/− SD. p values were calculated using an unpaired, two-tailed t test. For Source data are provided as a Source data file.

Article Snippet: Additional surface marker antibodies were CD45-89Y (Fluidigm; 3089003B), CD207-175Lu (Fluidigm; 3175016B), CD279-155Gd (Fluidigm; 3155009B), CD8a-146Nd (Fluidigm; 3146001B), TIM-3-153Eu (Fluidigm; 3153008B), TIGIT-209Bi (Fluidigm; 3209013B), and CD274-156Gd (Fluidigm; 3156026B).

Techniques: Marker, Flow Cytometry, RNAscope, Staining, Two Tailed Test

Journal: Nature Communications

Article Title: Skin basal cell carcinomas assemble a pro-tumorigenic spatially organized and self-propagating Trem2+ myeloid niche

doi: 10.1038/s41467-023-37993-w

Figure Lengend Snippet: a Diagram of transplantation strategies of male primary tumor into female NOD SCID mice. b RNAScope images of transplants showing male-specific Uty + (red) F4/80 + (green) macrophages within the tumor. Yellow arrows point to F4/80 + Uty + cells. Image is representative of n = 2 independent tumors. c Diagram of transplantation strategies and the ability to trace SCAMs from primary tumor using the CD45.2 allelic variant. d Summary of the proportions for the CD45.2 − and Cd45.2 + from either Cd11b + (left) or Cd11b + Trem2 + cells in the P0, P1, and P2 tumors. e Diagram summarizing self-propagating logic with approximate cell numbers. f Flow cytometry for Trem2 cells in the Cd11b + Cd45.2 + fractions from P0 and P1 tumors. g Quantification of the Trem2% of the Cd11b + Cd45.2 + and Cd11b + Cd45.2 - form the P0, P1, and P2 tumors. h Diagram of the transplantation strategy and subsequent sorting to isolate Cd45.2+ and CD45.2- cells from the P1 tumors for scRNA-Seq. i UMAP plots showing the different clusters from the Cd45.2+ and CD45.2- cells. j Feature plots showing key genes associated with SCAMs. k Violin plots showing key genes associated with SCAMs. l Diagram of the intratumor monocyte maturation injection strategy and subsequent analysis by flow cytometry. m Flow cytometry analysis of the injected GFP + monocytes for SCAM-specific markers. n Quantification of the SCAM-specific markers Trem2 and Vcam1 ( n = 4 independent injections into 4 different tumors). Length of each scale bar is noted in figure. For d , g , n = 4 tumors from P0, P1, and P2 allografts. Error bars represent mean +/− SD. p values were calculated using unpaired, two-tailed t test. Source data are provided as a Source data file.

Article Snippet: Additional surface marker antibodies were CD45-89Y (Fluidigm; 3089003B), CD207-175Lu (Fluidigm; 3175016B), CD279-155Gd (Fluidigm; 3155009B), CD8a-146Nd (Fluidigm; 3146001B), TIM-3-153Eu (Fluidigm; 3153008B), TIGIT-209Bi (Fluidigm; 3209013B), and CD274-156Gd (Fluidigm; 3156026B).

Techniques: Transplantation Assay, RNAscope, Variant Assay, Flow Cytometry, Injection, Two Tailed Test